SAXSdb — 1njt

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein P40

Human herpesvirus 5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–256 Chain B； UniProt 1–256	Fragment：Assemblin Mutation：A143Q	Peptidomimetic Inhibitor × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, HEPES, EDTA, Sodium Chloride, Sodium Sulfate, DTT, Spermine_HCl, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.271
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–256 Chain D； UniProt 1–256	Fragment：Assemblin Mutation：A143Q	Peptidomimetic Inhibitor × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, HEPES, EDTA, Sodium Chloride, Sodium Sulfate, DTT, Spermine_HCl, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.271

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1NJT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CMV HUMAN CYTOMEGALOVIRUS PROTEASE Deposited 1996-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Chain B 1–256（256 aa）	Mutation：V141A, A144P Mutation：V141A, A144P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；28-30% MONOMETHYL POLYETHYLENE GLYCOL 550 0.05-0.2 M NACL 10% GLYCEROL 50 MM HEPES AT PH 7.5	Resolution 2.27 Å R-free 0.310
1ID4 CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT (H157Q) OF THE HUMAN CYTOMEGALOVIRUS PROTEASE Deposited 2001-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Fragment：RESIDUES 1-256 Chain B 1–256（256 aa） Fragment：RESIDUES 1-256	Mutation：A143Q, H157Q Mutation：A143Q, H157Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；19% PEG 3350, 0.1M MES 6.0, 15% Glycerol, 5% t-BuOH, 0.4M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.262
1IEC CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT (H157A) OF THE HUMAN CYTOMEGALOVIRUS PROTEASE Deposited 2001-04-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Fragment：RESIDUES 1-256 Chain B 1–256（256 aa） Fragment：RESIDUES 1-256	Mutation：A143Q, H157A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：A143Q, H157A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；20% PEG3350, 0.1M MES 6.0, 15% GLYCEROL, 5% t-BuOH, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.269
1IED CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT (H157E) OF THE HUMAN CYTOMEGALOVIRUS PROTEASE Deposited 2001-04-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Fragment：RESIDUES 1-256 Chain B 1–256（256 aa） Fragment：RESIDUES 1-256	Mutation：A143Q, H157E Mutation：A143Q, H157E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；21% PEG3350, 0.1M MES 6.0, 15% GLYCEROL, 5% t-BuOH, 0.4M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.269
1IEF CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT S134A OF THE HUMAN CYTOMEGALOVIRUS PROTEASE Deposited 2001-04-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Fragment：RESIDUES 1-256 Chain B 1–256（256 aa） Fragment：RESIDUES 1-256	Mutation：A143Q, S134A Mutation：A143Q, S134A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；20% PEG3350, 0.1M MES 6.0, 15% GLYCEROL, 5% t-BuOH, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.30 Å R-free 0.270
1IEG CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT S134A/H157A OF THE HUMAN CYTOMEGALOVIRUS PROTEASE Deposited 2001-04-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Fragment：RESIDUES 1-256 Chain B 1–256（256 aa） Fragment：RESIDUES 1-256	Mutation：A143Q, S134A, H157A Mutation：A143Q, S134A, H157A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；19% PEG3350, 0.1M MES 6.0, 15% GLYCEROL, 5% t-BuOH, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.259
1JQ6 HUMAN CYTOMEGALOVIRUS PROTEASE DIMER-INTERFACE MUTANT, S225Y Deposited 2001-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa）	Mutation：A143Q, S225Y Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；294 K；PEG 8000, sodium cacodylate, magnesium acetate, glycerol, spermine tetrahydrochloride, DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.30 Å R-free 0.286
1JQ7 HCMV protease dimer-interface mutant, S225Y complexed to Inhibitor BILC 408 Deposited 2001-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Chain B 1–256（256 aa）	Mutation：A143Q, S225Y Mutation：A143Q, S225Y	0FP N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；PEG 4000, HEPES, sodium chloride, glycerol, spermine tetrahydrochloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.00 Å R-free 0.339
1LAY CRYSTAL STRUCTURE OF CYTOMEGALOVIRUS PROTEASE Deposited 1996-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa）	Mutation：A143V	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1NJU Complex structure of HCMV Protease and a peptidomimetic inhibitor Deposited 2003-01-02	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Chain B 1–256（256 aa）	Mutation：A143Q Mutation：A143Q	0FP N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, HEPES, EDTA, Sodium Chloride, Sodium Sulfate, DTT, Spermine_HCl, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.273
1NJU Complex structure of HCMV Protease and a peptidomimetic inhibitor Deposited 2003-01-02	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–256（256 aa） Chain D 1–256（256 aa）	Mutation：A143Q Mutation：A143Q	0FP N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, HEPES, EDTA, Sodium Chloride, Sodium Sulfate, DTT, Spermine_HCl, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.273
1NJU Complex structure of HCMV Protease and a peptidomimetic inhibitor Deposited 2003-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–256（256 aa） Chain B 1–256（256 aa） Chain C 1–256（256 aa） Chain D 1–256（256 aa）	Mutation：A143Q Mutation：A143Q Mutation：A143Q Mutation：A143Q	0FP N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, HEPES, EDTA, Sodium Chloride, Sodium Sulfate, DTT, Spermine_HCl, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.273
1NKK COMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR Deposited 2003-01-03	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–256（256 aa） Fragment：Assemblin Chain B 1–256（256 aa） Fragment：Assemblin	Mutation：A143Q, E31R Mutation：A143Q, E31R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, HEPES, EDTA, Sodium Chloride, Sodium Sulfate, DTT, Spermine_HCl, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.280
1NKK COMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR Deposited 2003-01-03	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–256（256 aa） Fragment：Assemblin Chain D 1–256（256 aa） Fragment：Assemblin	Mutation：A143Q, E31R Mutation：A143Q, E31R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, HEPES, EDTA, Sodium Chloride, Sodium Sulfate, DTT, Spermine_HCl, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.280
1NKM Complex structure of HCMV Protease and a peptidomimetic inhibitor Deposited 2003-01-03	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Chain B 1–256（256 aa）	Mutation：A143Q Mutation：A143Q	0FP N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, HEPES, EDTA, Sodium Chloride, Sodium Sulfate, DTT, Spermine_HCl, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.298
1WPO HYDROLYTIC ENZYME HUMAN CYTOMEGALOVIRUS PROTEASE Deposited 1996-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Chain B 1–256（256 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.288
2WPO HCMV protease inhibitor complex Deposited 1998-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–256（256 aa） Chain B 1–256（256 aa）	Mutation：A143Q, T181M, L229M Mutation：A143Q, T181M, L229M	01E (2S)-2-(3,3-dimethylbutanoylamino)-N-[(2S)-1-[[(2S,3S)-3-hydroxy-4-[(4-iodophenyl)methylamino]-4-oxo-butan-2-yl]amino]- 1,4-dioxo-4-pyrrol-1-yl-butan-2-yl]-3,3-dimethyl-butanamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.70 Å R-free 0.332
2WPO HCMV protease inhibitor complex Deposited 1998-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–256（256 aa） Chain D 1–256（256 aa）	Mutation：A143Q, T181M, L229M Mutation：A143Q, T181M, L229M	01E (2S)-2-(3,3-dimethylbutanoylamino)-N-[(2S)-1-[[(2S,3S)-3-hydroxy-4-[(4-iodophenyl)methylamino]-4-oxo-butan-2-yl]amino]- 1,4-dioxo-4-pyrrol-1-yl-butan-2-yl]-3,3-dimethyl-butanamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.70 Å R-free 0.332
9Y7L HCMV Protease in complex with Fab5 - Class 1 Deposited 2025-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–256（256 aa）	Mutation：A143V, A209V	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；25 mM potassium phosphate, 150 mM potassium chloride, pH 8.0 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9Y7M HCMV Protease in complex with Fab5 - Class 2 Deposited 2025-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–256（256 aa）	Mutation：A143V, A209V	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；25 mM potassium phosphate, 150 mM potassium chloride, pH 8.0 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.57 Å
9Y7N HCMV Protease in complex with Fab5 - Class 3 Deposited 2025-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–256（256 aa）	Mutation：A143V, A209V	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；25 mM potassium phosphate, 150 mM potassium chloride, pH 8.0 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.69 Å

17 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VP40_HCMVA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–256； UniProt 1–256 Author chain B； PDBConstruct 1–256； UniProt 1–256 Author chain C； PDBConstruct 1–256； UniProt 1–256 Author chain D； PDBConstruct 1–256； UniProt 1–256

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1njt
Deposition date deposition_date	2003-01-02
Structure title title	COMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR
Keywords keywords	PROTEASE, PEPTIDOMIMETIC INHIBITOR, INDUCED-FIT, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.21 Å
Radius of gyration Rg (electron density) rg_electron	35.76 Å
Forward intensity I(0) i0	169898000.00
Molecular weight molecular_weight	102330.0 kDa
Excluded volume excluded_volume	127020 Å³
Envelope volume envelope_volume	164840 Å³
Hydration-shell volume shell_volume	39273 Å³
Envelope diameter envelope_diameter	120.3 Å
Shell Rg shell_rg	41.02 Å
Envelope Rg envelope_rg	35.29 Å
Shape Rg shape_rg	35.77 Å
Total Rg total_rg	36.06 Å
Total atoms total_atoms	7201
Residues n_residues	906
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	120.1 Å
Rg (real space) rg_real	36.29 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	1.6990e+08
I(0) uncertainty (real space) i0_real_error	2.6020e+06
Rg (reciprocal space) rg_reciprocal	36.24 Å
I(0) (reciprocal space) i0_reciprocal	169900000.0000
Solution quality estimate total_estimate	0.6507
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.0 Å
Skewness Skewness skewness	0.306
Kurtosis Kurtosis kurtosis	-0.622
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	123500000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 0.028; Positv: 1.000; Valcen: 0.882; Smooth: 0.857

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Capsid protein P40
Molecular weight formula_weight	28130.5 kDa
EC 编号 ec_number	3.4.21.97
Mutation mutation	A143Q
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7444

MTMDEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEQATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA

来源 Source

来源生物 organism	Human herpesvirus 5
通用名 common_name	Human cytomegalovirus
NCBI Class编号 ncbi_taxonomy_id	10359
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptidomimetic Inhibitor
Molecular weight formula_weight	551.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

XVDNAX

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	243

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1njta_
Class class	b — All beta proteins
Fold Fold fold	b.57 — Herpes virus serine proteinase, assemblin
Superfamily Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
Family Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

Domain ID domain_id	d1njtb_
Class class	b — All beta proteins
Fold Fold fold	b.57 — Herpes virus serine proteinase, assemblin
Superfamily Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
Family Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

Domain ID domain_id	d1njtc_
Class class	b — All beta proteins
Fold Fold fold	b.57 — Herpes virus serine proteinase, assemblin
Superfamily Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
Family Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

Domain ID domain_id	d1njtd_
Class class	b — All beta proteins
Fold Fold fold	b.57 — Herpes virus serine proteinase, assemblin
Superfamily Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
Family Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

CATH v4.4 (4 domains)

Domain ID domain_id	1njtA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
Homologous superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

Domain ID domain_id	1njtB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
Homologous superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

Domain ID domain_id	1njtC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
Homologous superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

Domain ID domain_id	1njtD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
Homologous superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

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8. Citations (1)

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Unit-cell length a length_a	107.072 Å
Unit-cell length b length_b	213.306 Å
Unit-cell length c length_c	52.795 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	19.950 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2710

fit	/app/data/saxs_computation/nj/1njt/1njt.fit
pddf	/app/data/pr_computation/nj/1njt/1njt.pr.out
profile	/app/data/saxs_computation/nj/1njt/1njt.dat

COMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR

1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein P40

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)